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E323 Boxplots.R
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E323 Boxplots.R
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# E323 Boxplot Plotting
### Header
library (ggplot2)
### Import Data
setwd("C:/Users/grossar/Box/Sareen Lab Shared/Data/Vicky/E283-COVID Infection/Round 2 RNAseq/Analysis/")
viral.reads <- read.csv
mock.d1 = c(0,1,0)
infected.d1 = c(3530, 3751, 4114)
mock.d3 = c(0,0,0)
infected.d3 = c(20335,24292,25956)
reads = c(mock.d1, infected.d1, mock.d3, infected.d3)
condition = c("Day 1, Mock", "Day 1, Mock", "Day 1, Mock",
"Day 1, Infected", "Day 1, Infected", "Day 1, Infected",
"Day 3, Mock", "Day 3, Mock", "Day 3, Mock",
"Day 3, Infected", "Day 3, Infected", "Day 3, Infected")
data <- data.frame(mock.d1, infected.d1, mock.d3, infected.d3)
data <- data.frame(reads, condition)
ggplot(data = data, aes(x = condition, y = reads, color = condition)) +
geom_boxplot(size = 1.5, fill = "Grey80") +
scale_x_discrete(limits = c("Day 1, Mock", "Day 1, Infected", "Day 3, Mock", "Day 3, Infected")) +
scale_y_continuous(breaks = c(0,5000,10000,15000,20000, 25000)) +
scale_color_manual(values = c("#fab9b6", "#a6acf7", "#fe1c1c", "#000dc4")) +
labs(title = "Sequenced Reads by Condition",
x = "Condition",
y = "Number of Reads") +
theme(plot.title = element_text(color="black", face="bold", size=22, margin=margin(10,0,20,0)),
axis.title.x = element_text(face="bold", size=14,margin =margin(20,0,10,0)),
axis.title.y = element_text(face="bold", size=14,margin =margin(0,20,0,10)),
panel.background = element_rect(fill = 'white', color = 'black'),
plot.margin = unit(c(1,1,1,1), "cm"), axis.text = element_text(size = 12))
(g <- ggplot(count.pca.df, aes(PC1, PC2, color = time, fill = dose, shape = shape)) + geom_point(size = 4, stroke = 3) +
geom_text(aes(label=row.names(count.pca.df)),hjust=0,vjust=0) +
xlab(paste0("PC1: ",round(eig.val$variance.percent[1]),"% variance")) +
ylab(paste0("PC2: ",round(eig.val$variance.percent[2]),"% variance")) +
xlim(min(count.pca.df$PC1)-5,max(count.pca.df$PC1)+20) +
theme(plot.title = element_text(color="black", face="bold", size=22, margin=margin(10,0,20,0)),
axis.title.x = element_text(face="bold", size=14,margin =margin(20,0,10,0)),
axis.title.y = element_text(face="bold", size=14,margin =margin(0,20,0,10)),
panel.background = element_rect(fill = 'white', color = 'black'),
plot.margin = unit(c(1,1,1,1), "cm"), axis.text = element_text(size = 12)) +
ggtitle(paste(paste(perterbagen.to.include, collapse = ', '), '-', paste(cell.type.to.include))) +
scale_color_gradient(low="blue", high="red") +
scale_shape_manual(values = c(21, 25)) +
scale_fill_gradient(low="white", high="orange"))
# Boxplot of MPG by Car Cylinders
boxplot(mpg~cyl,data=mtcars, main="Car Milage Data",
xlab="Number of Cylinders", ylab="Miles Per Gallon")
library(ggplot2)
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth)
# Basic box plot
p <- ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot()
p
# Rotate the box plot
p + coord_flip()
# Notched box plot
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot(notch=TRUE)
# Change outlier, color, shape and size
ggplot(ToothGrowth, aes(x=dose, y=len)) +
geom_boxplot(outlier.colour="red", outlier.shape=8,
outlier.size=4)